[ccp4bb] PDBe Coordinator Position at EMBL-EBI
Dear All, We are looking for an outstanding individual to coordinate the Protein Data Bank in Europe team (PDBe; pdbe.org) team at the European Bioinformatics Institute (EMBL-EBI). This position is for an ambitious scientist, with a passion for open data, who wants to impact the development of key resources for global, public 3D-structure data. We need an inspiring and engaging person who understands the importance of teamwork and is focused on the delivery of key tasks. This is an opportunity for the right person to deliver significant impact in the area of 3D-structure data via PDBe data resources, tools and services. The closing date for this post is 22nd September 2023. For more information and to apply, visit: https://www.embl.org/jobs/position/EBI02160 Kind Regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Introducing ‘Covalently Linked Components’ and enriched ligand information at PDBe
Dear all, We are excited to announce the introduction of Covalently Linked Components (CLCs), a new class of reference small molecules that facilitates identification of covalently linked multi-component ligands across the whole PDB archive. This enhancement vastly improves the accessibility and usability of small molecule data for users. Alongside CLCs, we have further enriched the existing Peptide-like molecules Reference Dictionary (PRD) files by providing additional metadata, such as chemical properties and mapping between these molecules and other chemical data resources. As part of the update, we are also making changes to the PDBeChem FTP directory structure, aimed at enhancing user experience and making small molecule data in the Protein Data Bank in Europe (PDBe) more accessible. In this update, we have introduced separate folders for three types of reference files: Chemical Components (CCD), Covalently Linked Components (CLC), and Peptide-like molecules Reference Dictionary (PRD), making it easier for users to access specific data. The PDBeChem pipeline that powers this process and updates this data weekly, uses PDBe CCDUtils as its primary package. PDBe CCDUtils is an RDKit-based toolkit for handling and analysing small molecules in the PDB. For more information about CLC and these changes, visit:https://www.ebi.ac.uk/pdbe/news/introducing-covalently-linked-components <https://www.ebi.ac.uk/pdbe/news/introducing-covalently-linked-components> *Urgent Notice:* Effective from January 1st, 2024, we will be retiring the top-level sub-directories and files related to CCD (Chemical Components) as part of our ongoing updates. This decision has been made to streamline our data organisation and improve the user experience. Detailed information regarding this change is provided in the README.txt, accessible at:https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/README.txt <https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/README.txt>. We value your cooperation and understanding as we strive to improve our data infrastructure and user accessibility. Thankyou for your continued support. Kind Regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] PDBImages: A new, open-source macromolecular structure imaging pipeline
** *Dear all,* * The PDBe team, in collaboration with David Sehnal (NCBR, Masaryk University, Czech Republic), has developed a new data pipeline for generating images of macromolecular structures. The new tool, PDBImages, provides more consistent and scalable visualisation for a range of different macromolecular views. The PDBImages software is built using Mol* (https://molstar.org/viewer), a powerful, open-source software for interactive molecular visualisation in the browser. It leverages a 'headless' version of Mol*, enabling it to render images directly from the command line without a graphical interface. The use of Mol* provides many benefits to the pipeline, including the ease in generating images of large structures and the output of Mol* state files to enable interactive visualisation directly within the browser. PDBImages reads atomic XYZ coordinates from PDBx/mmCIF or binaryCIF files and constructs predefined views of the macromolecular structures. For each of these views it then outputs the following files: * Image files (PNG format) * Mol* state files - these allow replication of the view within the Mol* viewer * Metadata files (JSON format) If you are interested in using the PDBImages tool, it is available as an npm package (https://www.npmjs.com/package/pdb-images <https://www.npmjs.com/package/pdb-images>), with the code also available on GitHub (https://github.com/PDBeurope/pdb-images <https://github.com/PDBeurope/pdb-images>). Read more: https://www.ebi.ac.uk/pdbe/news/pdbimages-new-open-source-macromolecular-structure-imaging-pipeline <https://www.ebi.ac.uk/pdbe/news/pdbimages-new-open-source-macromolecular-structure-imaging-pipeline>* -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] 3D-Beacons update: Search for structural models by protein sequence
Dear ccp4bb, The 3D-Beacons resource has undergone some major improvements, including updates to the API and a new sequence search feature. The 3D-Beacons Network, originally announced in September 2021 <https://www.ebi.ac.uk/pdbe/news/3d-beacons-network-protein-structure-data-all-one-place>, brings together experimentally determined and predicted protein structure models, alongside relevant quality metrics, from several providers and makes them freely available in one place. The data are provided by a number of services, including the Protein Data Bank in Europe (PDBe), AlphaFold DB, SWISS-MODEL, Protein Ensemble Database (PED), Small Angle Scattering Biological Data Bank (SASBDB), Genome3D, and PDBe Knowledge Base (PDBe-KB). 3D-Beacons allows users to search using UniProt accession and access protein structure models from all these different providers in a standardised format. The 3D-Beacons resource has been updated to include some major improvements to the infrastructure and the public website (3d-beacons.org <https://3d-beacons.org/>). This includes an update to the API to support POST queries to the summary endpoint, up to a maximum of 10 accessions. The release also includes a brand new sequence search feature, allowing users to easily find relevant structures based on an input protein sequence. For more information, view the full news item at https://www.ebi.ac.uk/pdbe/news/3d-beacons-update-search-structural-models-protein-sequence Kind Regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Clustering of distinct protein conformations across the whole PDB archive
Dear ccp4bb, The PDBe team is excited to unveil a new process for identifying protein conformational states across the Protein Data Bank (PDB) archive. Using deterministic clustering, we have developed a data pipeline that offers unprecedented insights into the structural variability of proteins. The pipeline considers all proteins in the PDB with 100% sequence identity and calculates a global dissimilarity score called "GLOCON". Chains with similar scores are clustered together. This process enables us to explore the range of conformation across protein structures, capturing both minor conformational differences and large domain movements. The results of the data pipeline are available through PDBe-KB aggregated views of proteins. Users can visualise the results per UniProt accessions using the "3D view of superposed structures" button to explore the structures in the Mol* viewer. In a number of case studies, this clustering process can indicate significant biological relevance. Some case studies, such as hexokinase, aldose reductase and KaiB, demonstrate the ability of the pipeline to identify distinct protein conformations and shed light on their biological significance. To find out more, view the full news item at https://www.ebi.ac.uk/pdbe/news/illuminating-protein-conformational-landscapes-pdb-archive We also encourage you to view our pre-print at https://doi.org/10.1101/2023.07.13.545008 If you have any questions or would like further details, please feel free to contact the team at pdbeh...@ebi.ac.uk. Kind regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] A new process for aggregating and naming assemblies in the PDB
Dear ccp4bb, PDBe has created a new process to aggregate and name assemblies in the PDB based on unique assembly composition. This process allows assemblies with the same composition to be aggregated together. The assemblies can be aggregated into over 90,000 distinct compositions by mapping each component in an assembly to external databases. Over 90% of the assemblies have been named using external resources such as Complex Portal, Gene Ontology, UniProt and manual curation by PDBe annotators. This new process will allow researchers to find all assemblies that have a certain UniProt/Rfam accession or combination of accessions. Users can also find super-assemblies of an assembly which can help understand how different protein complexes interact with each other. Finally, users can find assemblies based on specific names helping to identify and study specific protein complexes that are relevant to their research. Find out more at https://www.ebi.ac.uk/pdbe/news/new-process-aggregating-and-naming-assemblies-pdb Kind Regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] choosing an NMR structure from PDB
Hi Harry, A useful starting point when looking for the 'best' [insert criteria here] structure in the PDB for a specific protein is to visit the PDBe-KB aggregated views pages (https://pdbekb.org). These pages group PDB data based upon UniProt accession and the 'structures' tab on these pages shows all the available PDB entries containing this protein, as well as other resources that provide structural data for this protein (including some 'new-fangled predicted models'). For your UniProt ID, the relevant page is https://www.ebi.ac.uk/pdbe/pdbe-kb/proteins/P01132/structures. The list of of PDB entries is sorted to have the 'best' structure at the top - in this case, weighted by a combination of UniProt coverage, resolution (for X-ray/EM) and validation. It also displays information on resolution (if applicable), any bound ligands etc. to give this context to help in choosing a suitable structure. As you mention, for your example these are all NMR entries containing similar sized fragments of the full length UniProt sequence, so the ordering is predominantly using validation data to sort these. Unfortunately, in your case the most recent entry was before mandatory deposition of chemical shifts, so you do not have the option of experimental validation which is now available for recently deposited NMR entries. Therefore these are all ordered based on geometric validation. So, although there is no concrete answer to your question, the above process should help in filtering the options. Kind Regards, David On 03/05/2023 11:45, Harry Powell wrote: Hi folks I was wondering. If there is a UniProt entry (for example, P01132, but there are plenty of others) for which I want the “best” (whatever that might mean) representative _experimental_ structure (i.e. not one of these new-fangled predicted models that some folk say have removed the need for actually doing experiments), but there are only NMR models - how do I choose? I don’t mean “which model from the ensemble do I choose” - that’s a different question. For P01132, for example, I could choose (from the PDB) 1A3P, 1EGF, 1EPG, 1EPH, 1EPI, 1EPJ, 1GK5 or 3EGF. Note that some of these are from the same paper, so may be in different conditions (e.g. pH). All except the first (1A3P) cover the same bit of sequence. Specifically, what should I look for in the downloadable files (mmCIF, for example) from the PDB? Thoughts? Harry To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Removal of ls-lR index file from the PDB archive
Dear PDB-l, With continuing growth of the PDB archive, the size of the file that lists all directory contents (currently https://files.wwpdb.org/pub/pdb/ls-lR) will become a challenge for long term maintenance. wwPDB plans to remove this file from the PDB archive at 00:00 UTC on July 12, 2023. We strongly encourage users to utilize files previously announced that containing the same data (https://files.wwpdb.org/pub/pdb/holdings/). These inventory data files offer a quick overview of data in the archive. These files are in the extensible JSON format, and can be found under the new /pdb/holdings/ archive tree. The inventory lists provided include: * all_removed_entries.json.gz: a list of obsoleted PDB entries including information for entry authors, entry title, release date, obsolete date, and superseding PDB ID, if any. * current_file_holdings.json.gz: a list of released PDB entries and the file types present for each in the PDB Core Archive (e.g. coordinate data, experimental data, validation report). * obsolete_structures_last_modified_dates.json.gz: a list of obsoleted PDB entries with information about the most recent modification date of the PDBx/mmCIF file. * refdata_id_list.json.gz: a list of released chemical reference entries, their content types (e.g., Chemical Component, BIRD), and the most recent modification date of the reference file. * released_structures_last_modified_dates.json.gz: a list of released PDB entries with the most recent modification date of the PDBx/mmCIF file. * unreleased_entries.json.gz: a list of on-hold PDB entries, their entry status, deposition date, and pre-release sequence information, where available. Users are encouraged to utilize these inventory files. For example, checking for the update of the PDB archive can be performed using current_file_holdings.json.gz <https://s3.rcsb.org/pub/pdb/holdings/current_file_holdings.json.gz> or released_structures_last_modified_dates.json.gz <https://s3.rcsb.org/pub/pdb/holdings/released_structures_last_modified_dates.json.gz> in /pub/pdb/holdings/. Please contact i...@wwpdb.org with any questions. -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Updated pipeline for small molecule data processing at PDBe
** *We have updated the tools used at PDBe and PDBe-KB for processing small molecule ligands and their interactions in the PDB archive. This process now identifies larger, linked ligands that are composed of individual components covalently linked together, allowing these molecules to be identified in a standardised manner for the first time.* * The ‘pdbeccdutils’ python library (https://github.com/PDBeurope/ccdutils) has been developed for the processing of small molecules in the PDB and this update sees a number of improvements to the pipeline. This process is used to generate data in PDBe’s updated CCD files, including standard 2D and 3D depictions, fragment and scaffold identification, external database mapping, and more. The updates to pdbeccdutils includes the addition of a new module to determine ‘bound molecules’, defined as multiple, covalently linked CCD ligands into a single, larger molecule. There are also updates to the underlying packages, including use of RDKit 2022.09.x for generating molecular properties, and use of Gemmi for parsing PDBx/mmCIF format files. There is one breaking change, which is the replacement of ccd_cif_dict with ccd_cif_block in the updated CCD files. There have also been updates to PDBe Arpeggio, our version of Arpeggio, a python library originally developed by the Blundell group. The PDBe Arpeggio python library generates interactions data for proteins and ligands in the PDB archive. This update to v1.5 includes improvements in identification of different molecule types and updates to underlying packages, including Open Babel v3.0.0 and inclusion of Gemmi for parsing PDBx/mmCIF files. For more information about the updates to pdbeccdutils and PDBe Arpeggio, view the full news item at https://www.ebi.ac.uk/pdbe/news/updated-pipeline-small-molecule-data-processing-pdbe <https://www.ebi.ac.uk/pdbe/news/updated-pipeline-small-molecule-data-processing-pdbe> Kind Regards, David Armstrong * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Helping improve AlphaFold DB - survey on similarity searches
** *Dear list, * * The AlphaFold Protein Structure Database (https://www.alphafold.ebi.ac.uk <https://www.alphafold.ebi.ac.uk>) team are excited to announce plans to expand the database’s capabilities, and we need your help with it. We seek feedback on how you perform protein similarity searches, which will help us build more effective and helpful sequence and structure-based searches. If you’re interested, please fill in the survey https://forms.gle/pwjsmgmJWz9QR7X47 <https://forms.gle/pwjsmgmJWz9QR7X47>. It will take no more than 4 minutes. Thank you for your time and interest! As we progress on this project, we will keep the community updated. * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Enriched chemical component files at PDBe
For users looking to access data on the small molecules in the PDB archive, the wwPDB chemical component dictionary (CCD) provides detailed information about geometry and linkage information for these ligands. To provide even more detailed information about these molecules, the PDBe team has created a process to provide enriched, updated versions of these CCD files, providing additional data. These files are available through the PDBe FTP area at the following URL: http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/ with the folders constructed based upon the first character of the CCD ID, followed by the full length CCD ID, for example: http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/S/STI/STI.cif The additional data provided in the PDBe updated CCD files includes information on links to external databases generated through the UniChem service, including identifiers for ChEMBL, ChEBI, BindingDB, KEGG and more. This process also generates more extensive synonym information from these related databases. There is also mapping to DrugBank IDs, providing information on drug classification and its protein targets. There is also data provided on chemical structure, with information about Murcko scaffolds and fragments for the molecule. Furthermore, we also provide a number of physicochemical properties through these files, based on analysis with the RDKit (https://www.rdkit.org/) software. These physicochemical properties include information such as number of rotatable bonds, number of hydrogen bonds/acceptors and many more. Finally we also make available 2D atom coordinates and bond order required to create standardised images of the molecule. This information is used to display the ligands on our 2D ligand interactions component on the PDBe website (e.g. ibuprofen binding site in PDB entry 3p6h: https://www.ebi.ac.uk/pdbe/entry/pdb/3p6h/bound/IBP). The ligand interactions component displays the ligand chemical structure, highlighting interactions with other components in the structure. Users can also find idealised 3D conformers generated using RDKit in these updated CCD files. Kind Regards, David Armstrong -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Reminder: AlphaFold DB bioinformatics training role at EMBL-EBI - deadline 15th Jan
*We are recruiting for a bioinformatician to develop training for the AlphaFold Protein Structure Database (AlphaFold DB), as part of the Velankar team at the European Bioinformatics Institute (EMBL-EBI).* * This is an exciting opportunity to work as part of EMBL and DeepMind's new partnership to make the most complete and accurate database of predicted protein structures freely and openly available to the scientific community. The successful candidate will design and develop training for the AlphaFold DB, liaise with user communities, promote training materials, and publicly represent AlphaFold DB at various training events. There is the option for a part time role in this position. Deadline: 15th January 2023 For more information on this role and to apply, visit https://pdbe.org/jobs. Kind Regards, David Armstrong * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Software Infrastructure Engineer role available at PDBe
** *We are recruiting for a Software Infrastructure Engineer to provide technical support to develop and deploy the PDBe and PDBe-KB web services within the broader ecosystem of EMBL-EBI and the wwPDB collaboration, as part of the Velankar team at the European Bioinformatics Institute (EMBL-EBI).* * The successful candidate will report directly to the PDBe team leader as a Technical Officer. This post is an opportunity for the right person to bring IT skills and innovative ideas to help sustain the growing amount of structural biology data in the PDB and ensure that PDBe and PDBe-KB services remain firmly placed on a sustainable footing. Deadline: 29th January 2023 For more information on this role and to apply, visit https://pdbe.org/jobs Kind Regards, David * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] AlphaFold DB bioinformatics training role available at EMBL-EBI
** *We are recruiting for a bioinformatician to develop training for the AlphaFold Protein Structure Database (AlphaFold DB), as part of the Velankar team at the European Bioinformatics Institute (EMBL-EBI).* * This is an exciting opportunity to work as part of EMBL and DeepMind's new partnership to make the most complete and accurate database of predicted protein structures freely and openly available to the scientific community. The successful candidate will design and develop training for the AlphaFold DB, liaise with user communities, promote training materials, and publicly represent AlphaFold DB at various training events. There is the option for a part time role in this position. Deadline: 15th January 2023 For more information on this role and to apply, visit https://pdbe.org/jobs. Kind Regards, David Armstrong * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Multiple AlphaFold DB jobs available at EMBL-EBI
** *We are currently recruiting for several positions at the AlphaFold Protein Structure Database (AlphaFold DB)to join the Velankar team at the European Bioinformatics Institute (EMBL-EBI).* * These are exciting opportunities to work as part of EMBL and DeepMind's new partnership to make the most complete and accurate database of predicted protein structures freely and openly available to the scientific community. The jobs are detailed below but for more information and to apply, visit https://pdbe.org/jobs. AlphaFold DB front-end developer A technical role, developing and maintaining user-facing web pages and developing innovative data visualizations that interact with the 3D molecular graphics viewer, Mol*. Deadline: 12th September 2022 AlphaFold DB search engine developer A technical role, further developing the search engine of AlphaFold DB, and designing and implementing ways to improve the information display, including improving the relevance of search hits. Deadline: 12th September 2022 AlphaFold DB UX/UI expert A technical role, designing and validating new user interface elements and improving existing ones, with responsibility for maintaining the graphics design asset library of AlphaFold DB. Deadline: 19th September 2022 AlphaFold DB Bioinformatician (Data Integration) A scientific, technical role, responsible for discovering, mapping and integrating sequence, structure and functional annotations for AlphaFold protein structure predictions. Deadline: 26th September 2022 AlphaFold DB Bioinformatician (Training) Design and develop training for the AlphaFold DB, liaise with user communities, promote training materials, and publicly represent AlphaFold DB at various training events. There is the option for a part time role in this position. Deadline: 26th September 2022 For more information on all these job roles and to apply, visit https://pdbe.org/jobs. * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Improved EM validation with Q-score at the PDB
Dear Colleagues, Starting September 23, wwPDB validation of 3DEM structures for which there is both a model and an EM volume will include the Q-score metric (Pintilie, G., et al., 2020, Nat. Methods). This follows recommendations from the wwPDB/EMDB workshop on cryo-EM data management, deposition and validation in 2020 (white paper in preparation), as well as EM Validation Challenge events (Lawson C., et al., 2020, Struct. Dyn.; Lawson, et al., 2021, Nat. Methods). This will be the first quantitative parameter of residue and chain resolvability for EM maps in wwPDB validation reports and will provide an additional map-model assessment criterion. The Q-score calculates the resolvability of atoms by measuring the similarity of the map values around each atom relative to a Gaussian-like function for a well-resolved atom. A Q-score of 1 indicates that the similarity is perfect whilst closer to 0 indicates the similarity is low. If the atom is not well placed in the map then a negative Q-score value may be reported. Therefore, Q-score values in the reports will be in a range of -1 to +1. The wwPDB EM validation reports will provide Q-scores for single particle, helical reconstruction, electron crystallography, and subtomogram averaging entries for which both an EM map and coordinate model have been deposited. Validation reports (PDF files) will contain images of the average per-residue Q-scores colour-mapped onto ribbon models with views from three orthogonal directions. Similar images will also be introduced to visualize the per-residue atom-inclusion scores. A comparison of these two sets of images will assist in the visual assessment of the model-to-map fit and quality. Please refer to the wwPDB news article for example images: http://www.wwpdb.org/news/news?year=2022#62de9e5235ec5bb4ddb19a43 The validation reports will also contain a table of average per-chain values of both metrics (Q-score and atom inclusion) as well as their overall average values for the entire model. The per-residue and the per-chain average atom-inclusion and Q-score values will also be provided in the mmCIF and XML formatted validation files. The mmCIF categories _pdbx_vrpt_summary_entity_fit_to_map and _pdbx_vrpt_model_instance_map_fitting will be introduced to include both the Q-scores and atom-inclusion values. The existing items, _pdbx_vrpt_summary_entity_geometry.average_residue_inclusion and _pdbx_vrpt_model_instance_geometry.residue_inclusion for atom inclusion will no longer be used. The PDB Core Archive holds validation reports that assess each 3DEM model in the PDB along with the associated experimental 3D volume in EMDB. Validation reports of 3DEM structures (map and model) can be downloaded at the following wwPDB mirrors: * wwPDB: https://ftp.wwpdb.org/pub/pdb/validation_reports/ * RCSB PDB: https://ftp.rcsb.org/pub/pdb/validation_reports/ * PDBe: https://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ * PDBj: https://ftp.pdbj.org/pub/pdb/validation_reports/ The EMDB Core Archive holds validation reports that assess each EMDB map/tomogram entry. Validation reports for all EMDB volumes can be downloaded at the following wwPDB mirrors: * EMDB: https://ftp.ebi.ac.uk/pub/databases/emdb/validation_reports/ * wwPDB: https://ftp.wwpdb.org/pub/emdb/validation_reports/ * RCSB PDB: https://ftp.rcsb.org/pub/emdb/validation_reports/ * PDBj: https://ftp.pdbj.org/pub/emdb/validation_reports/ Additional information about validation reports is available for EM map+model, EM map-only, and EM tomograms. If you have any questions or queries about wwPDB validation, please contact us at validat...@mail.wwpdb.org. Best regards, James Tolchard -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Off-topic: Mol* Viewer re-centring hack
Hi Jon, Glad to see you are making use of the Mol* viewer. I am also replying on-list as others will hopefully find my response useful. For your specific case, I would recommend using the 'selection mode' - activated by clicking the cursor icon at the top right of the viewport. This mode changes the left-click action to a 'selection' of regions of the 3D structure, depending on the picking level defined in the selection toolbar (e.g. residue, atom, chain etc.). Once this mode is activated, clicking away from the structure will no longer reset the view - it will also enable you to create bespoke selections for e.g. visualisations or measurements. There is more information on selections in Mol* and much more in the Mol* Viewer documentation at https://molstar.org/viewer-docs There is also a recent webinar by one of my PDBe colleagues James Tolchard, which covers use of the PDBe implementation of the Mol* viewer. This may also give a good background for those new to using Mol*. You can access the webinar at https://youtu.be/13qSb1_3VWE Please feel free to contact me off-list if anyone is interest in learning more about the Mol* implementation at PDBe and queries about the use of the viewer. Kind Regards, David Armstrong On 28/06/2022 10:36, Read, Jon wrote: I have been using Mol* recently which looks like a really nice tool for basic model viewing. When you click off an atom (which is the normal action for clearing a selection in model viewers), it changes the zoom, orientation and re-slabs it. Has anyone found a hack to stop it re-centring/zooming/slabbing when you click off an atom. *Jon Read* AstraZeneca UK Limited is a company incorporated in England and Wales with registered number:03674842 and its registered office at 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0AA. This e-mail and its attachments are intended for the above named recipient only and may contain confidential and privileged information. If they have come to you in error, you must not copy or show them to anyone; instead, please reply to this e-mail, highlighting the error to the sender and then immediately delete the message. For information about how AstraZeneca UK Limited and its affiliates may process information, personal data and monitor communications, please see our privacy notice at www.astrazeneca.com <https://www.astrazeneca.com> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Reminder: Data Visualisation Software Engineer position at PDBe
Dear Colleagues, We are looking to recruit a software engineer who is interested in advanced data visualisation tools for 3-dimensional macromolecular structure data to join the Protein Data Bank in Europe (PDBe) team at the European Bioinformatics Institute (EMBL-EBI). This is a collaborative project between PDBe and RCSB Protein Data Bank. This is a technical role, working together with developers and curators from PDBe and RCSB PDB to create infrastructure for integrating multi-scale macromolecular structure data and providing FAIR access to these data. You will expand the 3-dimensional graphics viewer, Mol*, and will create novel data visualisation tools that will power the web applications of several core data resources. The closing date for this post is 13th May 2022. For more information on the position, please visit: https://www.ebi.ac.uk/pdbe/about/jobs Kind regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Reminder: Bioinformatician/Scientific Programmer position at PDBe
A reminder of this open position for a Bioinformatician/Scientific Programmer in the PDBe team: We have an exciting opportunity for a structural bioinformatician interested in the intersection of bioinformatics and cheminformatics to join the Protein Data Bank in Europe (PDBe) team at the European Bioinformatics Institute (EMBL-EBI) on a 2-year collaborative project between PDBe, ChEMBL and CCDC. The work includes improving data processing pipelines to increase the mapping between these data resources, performing data analysis, and contributing to developing web applications and user-facing web pages for PDBe and PDBe-KB. The closing date for this post is 3rd May 2022. For more information and to apply, visit: https://www.embl.org/jobs/position/EBI02000 Kind Regards, David Armstrong -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Bioinformatician/Scientific Programmer position at PDBe
We have an exciting opportunity for a structural bioinformatician interested in the intersection of bioinformatics and cheminformatics to join the Protein Data Bank in Europe (PDBe) team at the European Bioinformatics Institute (EMBL-EBI) on a 2-year collaborative project between PDBe, ChEMBL and CCDC. The work includes improving data processing pipelines to increase the mapping between these data resources, performing data analysis, and contributing to developing web applications and user-facing web pages for PDBe and PDBe-KB. The closing date for this post is 3rd May 2022. For more information and to apply, visit: https://www.embl.org/jobs/position/EBI02000 Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Bioinformatician position at PDBe - closing Friday
Dear Colleagues, We are looking to recruit a structural bioinformatician who is interested in protein domains and functional annotations to join the Protein Data Bank in Europe (PDBe) team at the European Bioinformatics Institute (EMBL-EBI). This is a collaborative project between PDBe, the SCOP team at the MRC Laboratory of Molecular Biology (LMB). This is a technical role, working together with developers and curators from PDBe and SCOP to improve a domain assignment tool, improve and further automate domain identification in multi-domain proteins, and help expand fold libraries. The successful candidate will also contribute to designing and implementing PDBe-KB web pages focused on aggregating structural data for specific structure domains. The closing date for this post is 25th March 2022. For more information on the position, please visit: https://www.ebi.ac.uk/pdbe/about/jobs Kind regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Deposition of half-maps for certain EM entries now mandatory for EMDB deposition
Dear CCP4, Deposition of half-maps for single-particle, single-particle-based helical, and sub-tomogram averaging reconstructions to the EM Data Bank (EMDB), as announced previously in https://www.wwpdb.org/news/news?year=2021#61afa92e5f450743ba4aa438, has now become mandatory. This change is in response to a long-standing community request to the wwPDB EMDB Core Archive and was also a recommendation from the 2020 wwPDB single-particle cryo-EM data-management workshop (white paper in preparation). Several recommendations from this workshop have already been implemented in the wwPDB OneDep system. These include improvements to wwPDB validation reports <https://www.wwpdb.org/news/news?year=2021#5ffc647df32c497fd6f7bf65> and enhancements for capturing metadata via the deposition interface. Mandatory half-maps must be unfiltered, unmasked, unsharpened, and positioned in the same coordinate-space and orientation as the primary map such that they superimpose. The availability of half-maps will contribute to improved validation of EM structures as reflected in the wwPDB validation reports. wwPDB strongly urges developers of cryo-EM processing software for the affected modalities to implement support for output of such half-maps (if this is not already available). Any queries about this policy change can be directed to i...@wwpdb.org. Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] PDBe updated mmCIF files now available via FTP
Dear Colleagues, PDBe has madePDBx/mmCIF files, containing SIFTS mapping information and additional, standardised metadata available directly from the EMBL-EBI FTP area, from: https://ftp.ebi.ac.uk/pub/databases/msd/updated_mmcif/ PDBe’s release process creates these enriched PDBx/mmCIF files from PDB archive files, containing more consistent, standardised metadata, without altering core PDB information, such as atomic coordinates and experimental data. These PDBx/mmCIF files have recently been further enriched with data from the SIFTS process <https://www.ebi.ac.uk/pdbe/about/news/sifts-data-now-included-pdbe-mmcif-files>, providing improved mapping between structure and sequence data. These enriched PDBx/mmCIF files are compressed and distributed from two subfolders in the FTP area. Firstly, you can efficiently access files for individual entries via the ‘divided’ folder, where each entry is placed within a folder identified by the second and third characters of the PDB entry ID (e.g. divided/at/1atp_updated.cif.gz). Alternatively, all the compressed updated PDBx mmCIF files in the PDB archive are available from the ‘all’ folder (e.g. all/1atp_updated.cif.gz). Alternatively, these files can also be downloaded from PDBe entry pages (https://www.ebi.ac.uk/pdbe/entry-files/download/7o9f_updated.cif). These files are also accessible via static URL (https://www.ebi.ac.uk/pdbe/static/entry/7o9f_updated.cif) or via PDBe bulk download service available at https://www.ebi.ac.uk/pdbe/download/api. If you have any queries about these files or how to access them, please contact our helpdesk at pdb...@ebi.ac.uk. Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Distributing PDBx/mmCIF Formatted Assembly Files at the PDB Core Archive
Dear ccp4bb, Starting May 3rd 2022, the PDB archive will distribute assembly files in PDBx/mmCIF format, allowing direct access and visualisation of the curated assemblies for all PDB entries. Currently, PDBx/mmCIF formatted assembly files are provided for structures that are non-PDB compliant, however the coordinates use model numbers to differentiate alternate symmetry copies of PDB chain IDs. This method is not ideal, nor necessary, for the current archive PDBx/mmCIF format and has lead to limited use of these files in community software tools. In response to this issue and recommendations by the wwPDB advisory committee, we are implementing updated, standardised practices for generation of assembly files for all PDB entries. These updated PDBx/mmCIF format assembly files will have improved organization of assembly data to support usage by the community. These files will include all symmetry generated copies of each chain within a single model, with distinct chain IDs (_atom_site.auth_asym_id and _atom_site.label_asym_id) assigned to each. Generation of distinct chain IDs in assembly files are based upon the following rules: * Chain IDs of the original chains from the atomic coordinate file will be retained (e.g., A) * Assign unique chain ID (atom_site.label_asym_id and atom_site.auth_asym_id) for each symmetry copy within a single model. Rules of chain ID assignments: o The applied index of the symmetry operator (pdbx_struct_oper_list.id) will be appended to the original chain ID separated by a dash (e.g., A-2, A-3, etc.) o If there are more than one type of symmetry operators applied to generate symmetry copy, a dash sign will be used between two operators (e.g., A-12-60, A-60-88, etc.) In addition, entity ID and chain ID mapping categories, _pdbx_entity_remapping and _pdbx_chain_remapping will be provided. A new directory, https://ftp.wwpdb.org/pub/pdb/data/assemblies/mmCIF/ <https://ftp.wwpdb.org/pub/pdb/data/assemblies/mmCIF/> will be created for the distribution of these updated assembly files. The directory containing the existing assembly mmCIF files for large entries will be removed (https://ftp.wwpdb.org/pub/pdb/data/biounit/mmCIF/ <https://ftp.wwpdb.org/pub/pdb/data/biounit/mmCIF/>). wwPDB asks all PDB users and software developers to review code and address any limitations related to PDB assemblies. Sample files are made available for testing purposes and to support community adoption at https://github.com <https://github.com/wwpdb/assembly-mmcif-examples>/wwpdb/assembly-mmcif-examples <http://github.com/wwpdb/assembly-mmcif-examples>. If you plan to use these assembly files for graphical viewing, check if your visualization software (e.g., PyMol, ChimeraX, etc.) supports instantiation of assemblies directly from atomic coordinate files (_struct_assembly related categories), you do so for improved efficiency. For any further information please email i...@wwpdb.org. <mailto:i...@wwpdb.org> Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Software Engineer position at PDBe
Dear Colleagues, We are looking to recruit a software engineer who is interested in advanced data visualisation tools for 3-dimensional macromolecular structure data to join the Protein Data Bank in Europe (PDBe) team at the European Bioinformatics Institute (EMBL-EBI). This is a collaborative project between PDBe and RCSB Protein Data Bank. This is a technical role, working together with developers and curators from PDBe and RCSB PDB to create infrastructure for integrating multi-scale macromolecular structure data and providing FAIR access to these data. You will expand the 3-dimensional graphics viewer, Mol*, and will create novel data visualisation tools that will power the web applications of several core data resources. The closing date for this post is 22nd February 2022. For more information on the position, please visit: https://www.ebi.ac.uk/pdbe/about/jobs Kind regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Bioinformatician position at PDBe - deadline extended to 9th Feb
Dear Colleagues, We have an exciting opportunity for a bioinformatician interested in structural biological data and functional annotations to work within the Protein Data Bank in Europe Team (PDBe) at the European Bioinformatics Institute (EMBL-EBI). The work includes standardising post translational modification information within the PDB archive in collaboration with wwPDB partners, plus integration and display of post-translational and proteomics data on the PDBe and PDBe-KB web pages. This is a collaboration with the PRIDE data resource at EMBL-EBI and Juri Rappsibler team at the University of Edinburgh. The closing date for this post has been extended to 9th February 2022. For more information on the position, please visit: https://www.embl.org/jobs/position/EBI01913 Kind regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Reminder: Bioinformatician position at PDBe - closing soon
Dear Colleagues, We have an exciting opportunity for a bioinformatician interested in structural biological data and functional annotations to work within the Protein Data Bank in Europe Team (PDBe) at the European Bioinformatics Institute (EMBL-EBI). The work includes standardising post translational modification information within the PDB archive in collaboration with wwPDB partners, plus integration and display of post-translational and proteomics data on the PDBe and PDBe-KB web pages. This is a collaboration with the PRIDE data resource at EMBL-EBI and Juri Rappsibler team at the University of Edinburgh. The closing date for this post is 26th January 2022. For more information on the position, please visit: https://www.embl.org/jobs/position/EBI01913 Kind regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] SIFTS sequence mappings now included in PDBe mmCIF files
Dear colleagues, Data on sequence level mapping through the SIFTS process <https://www.ebi.ac.uk/pdbe/docs/sifts/> can now be retrieved directly from updated mmCIF files, available on PDBe entry pages. These files now contain residue-level mapping between UniProt and PDB entries, including coordinate numbering for UniProt accessions and mapping to a host of other protein resources. PDBe’s release process creates ‘updated’ PDBx/mmCIF files from PDB archive files, containing remapped enumerations and additional information, while yielding more consistent, standardised metadata, without altering core PDB information, such as atomic coordinates and experimental data. These updated PDBx/mmCIF files have now been further enriched by the addition of three new ‘SIFTS- specific’ categories, providing improved mapping between structure and sequence data. SIFTS provides residue-level mapping between UniProt and PDB entries, while also incorporating annotation from the IntEnz, GO, InterPro, Pfam, CATH, SCOP, SCOP2, PubMed, Ensembl and Homologene resources. The information is updated and released every Wednesday concurrently with the release of new PDB entries and can be obtained from the PDBe Rest API <https://www.ebi.ac.uk/pdbe/api/doc/sifts.html> or PDB entry XML files in the EMBL-EBI FTP <ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/> area. Following this update to the updated PDBx/mmCIF files produced by PDBe, SIFTS data can also be directly retrieved from these files and are available from PDBe entry pages. For more information, visit https://www.ebi.ac.uk/pdbe/about/news/sifts-data-now-included-pdbe-mmcif-files Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Bioinformatician position at PDBe
Dear Colleagues, We have an exciting opportunity for a bioinformatician interested in structural biological data and functional annotations to work within the Protein Data Bank in Europe Team (PDBe) at the European Bioinformatics Institute (EMBL-EBI). The work includes standardising post translational modification information within the PDB archive in collaboration with wwPDB partners, plus integration and display of post-translational and proteomics data on the PDBe and PDBe-KB web pages. This is a collaboration with the PRIDE data resource at EMBL-EBI and Juri Rappsibler team at the University of Edinburgh to facilitate deposition of cross-linking data during PDB structure deposition. The closing date for this post is 26th January 2022. For more information on the position, please visit: https://www.embl.org/jobs/position/EBI01913 Kind regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] REMINDER: Bioinformatician position at PDBe - closing 4th November
A reminder of our exciting opportunity for a bioinformatician interested in structural biological data and functional annotations to work within the Protein Data Bank in Europe Team (PDBe) at the European Bioinformatics Institute (EMBL-EBI). The work includes standardising post translational modification information within the PDB archive in collaboration with wwPDB partners, plus integration and display of *post-translational modifications and proteomics data* on the PDBe and PDBe-KB web pages. This is a collaboration with the PRIDE data resource at EMBL-EBI and Juri Rappsibler team at the University of Edinburgh to facilitate deposition of cross-linking data during PDB structure deposition. The closing date for this post is *4th November 2021*. For more information on the position, please visit: https://www.embl.org/jobs/position/EBI01913 Kind regards, David -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Abstract submission deadline: 15th September - "50 Years of PDB" EMBL conference
*Join the EMBL conference “*Bringing Molecular Structure to Life: 50 Years of PDB*” and celebrate the 50th anniversary of The Protein Data Bank (PDB) with us. With over 1 million unique users worldwide and more than 400 biomedical data resources, the PDB represents the achievements and milestones of the structural biology community.* * The conference will be hosted virtually, running from 20th - 22nd October 2021. This timing coincides with the 50th anniversary of the original announcement of the PDB archive, when the structural biology community established the single worldwide archive for macromolecular structure data in 1971. *The abstract submission deadline is now 15th Sep 2021.* The archive is managed by the Worldwide Protein Data Bank consortium (wwPDB) which includes partner sites in Asia, Europe and America, making this a truly global effort. The 50th anniversary is an opportunity to celebrate the advances in structural biology and bioinformatics and peer into the future prospects for these fields. The session topics for the conference include: * Structural biology & applications in health and the environment * RNA/DNA molecular machines * Genomics meets structural biology * The next 50 years: future perspectives *Register and submit an abstract for the conference at s.embl.org/pdb21-01* Kind Regards, David Armstrong * -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Extended PDB IDs and PDB DOIs now available in PDBx/mmCIF files
Dear CCP4BB, wwPDB, in collaboration with the PDBx/mmCIF Working Group , has set plans <https://www.wwpdb.org/news/news?year=2021#607760112786e73a79c76f9d> to extend the length of ID codes for PDB and Chemical Component Dictionary (CCD) ID entries in the future. These extended formats are not supported by the legacy PDB file format. As announced previously <https://www.wwpdb.org/news/news?year=2017#5910c8d8d3b1d333029d4ea8>, wwPDB has extended PDB ID length to eight characters prefixed by ‘PDB’, e.g., pdb_1abc. Each PDB ID is issued a corresponding Digital Object Identifier (DOI), often required for manuscript submission to journals and described in publications by the structure authors. To help depositors provide information to journals, OneDep now displays the PDB ID and DOI on the submission confirmation page. The extended PDB IDs and corresponding PDB DOIs, along with existing four character PDB IDs, are now included in the PDBx/mmCIF formatted files. Initially, this will only be available for updated and newly-released PDB entries, with an archive-wide update at a later date. The additional accessions will be provided in the _database_2 PDBx/mmCIF category. For example, PDB entry 1ABC will have the extended PDB ID (pdb_1abc) and the corresponding PDB DOI (10.2210/pdb1abc/pdb). loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1abc pdb_1abc 10.2210/pdb1abc/pdb WWPDB D_1x ? ? Once all available four-character PDB IDs have been consumed, newly-deposited PDB entries will only be issued extended PDB ID codes. These entries will only be distributed in PDBx/mmCIF format. wwPDB asks journals, users, and software developers to review code and remove related limitations. Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Reminder: Bringing Molecular Structure to Life: 50 Years of the PDB closes abstract submission soon
View this email in your browser <https://us13.campaign-archive.com/?u=03514d4ffac1e7f3086502eab=eb574160eb=848f463a70> <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab=ecb8d84306=848f463a70> EMBL Conference *Bringing Molecular Structure to Life: 50 Years of the PDB* <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab=25c2ad0ee6=848f463a70> 20 – 22 October, Virtual Submit abstract by 25 August <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab=fbeebdbeef=848f463a70> Join this conference and celebrate the 50th anniversary of The Protein Data Bank (PDB) with us. With over 1 million unique users worldwide and more than 400 biomedical data resources, the PDB represents the achievements and milestones of the structural biology community. *Session topics:* * Structural biology and applications in health and the environment * RNA/DNA molecular machines * The next 50 years: Genomics meets structural biology * Latest advances * The next 50 years: Future perspectives Call for artwork An artwork exhibition will complement the conference, bringing awareness to the 50 year anniversary of the PDB. We are looking for creative scientists, wanting to exhibit their artwork representing scientific and/or societal concepts relating to a structure in the Protein Data Bank. F <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab=d4612c5461=848f463a70>ind out more <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab=f5f42dff90=848f463a70>>> <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab=b866915a66=848f463a70> Submit artwork by 4 August <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab=53e0c6af3a=848f463a70> One of the highlights of the meeting is the very timely session about *AlphaFold and the role of deep learning in structural biology *by John Jumper, DeepMind, UK*. * Read this article to learn more about the AI system: DeepMind and EMBL release the most complete database of predicted 3D structures of human proteins <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab=6f2223aa0f=848f463a70> <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab=54828f2b81=848f463a70> /Protein structures representing the data obtained via AlphaFold. Source image: AlphaFold. Design credit: Karen Arnott/EMBL-EBI/ Organisers Stephen Cusack, /EMBL Grenoble, France/ Gerard Kleywegt,/EMBL-EBI, UK/ Christoph Müller, /EMBL Heidelberg, Germany/ Christine Orengo, /University College London, UK/ Janet Thornton, /EMBL-EBI, UK/ Sameer Velankar, /EMBL-EBI, UK/ Matthias Wilmanns,/EMBL Hamburg, Germany/ Tweet #EMBLPDB <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab=1e4be5d072=848f463a70> Tweet #EMBLPDB <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab=54d5d55e92=848f463a70> Sponsor this event <mailto:sponsors...@embl.de> Sponsor this event <mailto:sponsors...@embl.de> Download the poster <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab=72f55264e0=848f463a70> Download the poster <https://embl.us13.list-manage.com/track/click?u=03514d4ffac1e7f3086502eab=cc2542e45a=848f463a70> -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Bringing Molecular Structure to Life: 50 Years of PDB - an EMBL conference
** *Join the EMBL conference “Bringing Molecular Structure to Life: 50 Years of PDB” and celebrate the 50th anniversary of The Protein Data Bank (PDB) with us. With over 1 million unique users worldwide and more than 400 biomedical data resources, the PDB represents the achievements and milestones of the structural biology community.* * The conference will be hosted virtually, running from 20th - 22nd October 2021. This timing coincides with the 50th anniversary of the original announcement of the PDB archive, when the structural biology community established the single worldwide archive for macromolecular structure data in 1971. The archive is managed by the Worldwide Protein Data Bank consortium (wwPDB) which includes partner sites in Asia, Europe and America, making this a truly global effort. The 50th anniversary is an opportunity to celebrate the advances in structural biology and bioinformatics and peer into the future prospects for these fields. The session topics for the conference include: * Structural biology & applications in health and the environment * RNA/DNA molecular machines * The next 50 years: Genomics meets structural biology * Latest advances * The next 50 years: future perspectives (part 1) * The next 50 years: future perspectives (part 2) Register for the conference at s.embl.org/pdb21-01 Deadlines: Abstract submission: 25 Aug 2021 Registration: 29 Sep 2021 Call for artwork An artwork exhibition will be part of the conference, bringing awareness to the 50th anniversary of the PDB. The conference participants can submit an artwork representing scientific and/or societal concepts relating to a structure in the Protein Data Bank. The artwork can be created using any technique or media, however, we will require a high-resolution image of the artwork for display in the virtual exhibition. Kind Regards, David Armstrong * -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] generate symmetry mates of EM structures
Dear Xiao, For public entries in the PDB archive, it is possible to download the coordinates of the assemblies defined in the PDB entry. If you visit the page for the entry at PDBe (pdbe.org/5l93) and select 'Downloads' you have the option to download various data, including mmCIF files containing the full assemblies. In this case, "Assembly 1 (mmCIF; gz)" would give you the full structure. Kind Regards, David Armstrong On 21/05/2021 11:33, Xiao Lei wrote: Dear Community, I wonder if there is a way to generate symmetry mates of EM structures? For example for PDB code 5L93, I tried PISA assembly server and Pymol to generate assembly (18 chains) but failed because it is not a crystal structure. I tried to download assembly directly from RCSB databank but after I opened the downloaded structure in Pymol, I can only see 3 chains, although the RCSB databank indicates the assembly should contain 18 chains. Best wishes and thank you in advance, Xiao To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] PDBe cif directories
Dear Bernhard, Thank you for pointing out this issue. We will update the links on our PDBe pages to direct to the updated chemical component files. In this case, the file redirection is incorrect and we will fix this. These new files contain all the information from the chemical component CIF files, however also include additional categories output from the PDBe CCD utils process (a wrapper of RDKit), including chemical properties and external cross reference mappings. If you have any further questions, please let us know at pdbeh...@ebi.ac.uk Kind Regards, David Armstrong On 04/02/2021 02:07, Bernhard Rupp wrote: Hi Fellows, do I see this correctly that on the main PDB page for a HET entry, such as https://www.ebi.ac.uk/pdbe/entry/pdb/4inx/bound/1EX <https://www.ebi.ac.uk/pdbe/entry/pdb/4inx/bound/1EX> the link in pulldown downloads/CIF dictionary ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/mmcif/1EX.cif <ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/mmcif/1EX.cif> dead ends in the old HET cif directory while from the PDBeChem https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/1EX <https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/1EX> the links goes to the new monomer library? ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/1/1EX/1EX.cif <ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/1/1EX/1EX.cif> Is the old pdbechem database now deprecated and only V2 current? Thx, BR -- Bernhard Rupp Crystallographiae Vindicis Militum Ordo http://www.hofkristallamt.org/ <http://www.hofkristallamt.org/> b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> +1 925 209 7429 +43 676 571 0536 -- Many plausible ideas vanish at the presence of thought -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Please help us improve our PDBe-KB aggregated views of proteins
Dear CCP4, To help us improve our PDBe-KB aggregated views of proteins, please fill in the following survey: https://tinyurl.com/y4vw8qkv <https://tinyurl.com/y4vw8qkv> The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org <https://pdbe-kb.org>) has recently released the latest update to its aggregated view of proteins (https://www.ebi.ac.uk/pdbe/about/news/superimposition-and-batch-downloads-added-pdbe-kb-aggregated-views <https://www.ebi.ac.uk/pdbe/about/news/superimposition-and-batch-downloads-added-pdbe-kb-aggregated-views>). These pages provide a comprehensive overview of structural data available in the PDB for a full-length protein sequence, with all the observed small-molecules interacting with the protein, all the macromolecular interaction sites and partners, and additional functional annotations, such as sequence conservation and effects of mutations. We are interested in your feedback and suggestions for further improving these aggregated views of proteins (https://pdbe-kb.org/proteins <https://pdbe-kb.org/proteins>) and for addressing potential gaps in their functionality or the data they offer. If you have any questions, please feel free to contact us directly. Kind regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] EMBL-EBI Structural Bioinformatics course (virtual) - Registration extended until 2nd October
Dear CCP4, We have extended the registration deadline for the virtual EMBL-EBI Structural Bioinformatics course until 2nd October 2020. This course explores bioinformatics data resources and tools for the investigation, analysis, and interpretation of biomacromolecular structures. It will focus on how best to analyse and interpret available structural data to gain useful information given specific research contexts. The course content will also cover predicting protein structure and function, and exploring interactions with other macromolecules as well as with low-MW compounds. This course will be a virtual event delivered via a mixture of live-streamed sessions, pre-recorded lectures, and tutorials with live support. For more information and to register, please visit bit.ly/EBI_sbr Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Help us design PDBe-KB's aggregated views of small molecules
PDBe-KB is a community-driven resource managed by the Protein Data Bank in Europe (PDBe) team, integrating functional annotations and structure data in the PDB archive. Recently, we started providingaggregated views <http://pdbekb.org/proteins>of available structure data and annotations for individual proteins. Now, we aim to develop similar aggregated views focusing on small molecules (i.e. ligands) in the PDB. We would like your help to understand what information regarding small molecules is useful to you by responding to thisshort survey <https://forms.gle/4Kk5kWLDyKUU5hwE9>. The full link to this feedback form is provided below: https://forms.gle/4Kk5kWLDyKUU5hwE9 Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Reminder - PDBe workshop: Making the most of PDB data with PDBe’s new graph database
Are you looking to use PDB data more effectively to answer complex scientific questions? Do you have experience of accessing data programmatically, but want to ask more complex questions? Then you will be interested in our EBI training workshop on accessing PDBe and PDBe-KB data using our new graph database. This workshop covers the use of the PDBegraph database <https://www.ebi.ac.uk/pdbe/pdbe-kb/schema>to extract data for solving complex structural biology queries. It will introduce the PDBe graph database and how to write Cypher queries to retrieve data of interest. Workshop participants will be able to use the graph database to explore data relevant to their own research with support and guidance from the development team at PDBe. For more information and to register, please visit www.ebi.ac.uk/training/events/2020/mining-pdbe-and-pdbe-kb-using-graph-database <http://www.ebi.ac.uk/training/events/2020/mining-pdbe-and-pdbe-kb-using-graph-database>. Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] PDBe workshop: Making the most of PDB data with our new graph database
Are you looking to use PDB data more effectively to answer complex scientific questions? Do you have experience of accessing data programmatically, but want to more easily create complex data queries? Then you will be interested in our EBI training workshop on accessing PDBe and PDBe-KB data using our new graph database. This workshop covers the use of the PDBegraph database <https://www.ebi.ac.uk/pdbe/pdbe-kb/schema>to extract data for solving complex structural biology queries. It will introduce the PDBe graph database and how to write Cypher queries to retrieve data of interest. Workshop participants will be able to use the graph database to explore data relevant to their own research with support and guidance from the development team at PDBe. For more information and to register, please visit www.ebi.ac.uk/training/events/2020/mining-pdbe-and-pdbe-kb-using-graph-database <http://www.ebi.ac.uk/training/events/2020/mining-pdbe-and-pdbe-kb-using-graph-database>. Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Improve your previously released coordinates with OneDep
Dear CCP4BB, The wwPDB are pleased to announce the availability of PDB versioning, allowing depositors to update their entries while retaining the same PDB accession code. Depositors can now submit new coordinates for existing entries. Initially, this is limited to PDB entries that were submitted via the OneDep system, which was introduced in 2014. The wwPDB plans to extend this functionality to entries deposited in the legacy systems (ADIT and Autodep) in future, and will announce a timeline for this in due course. Requests should be initiated using the OneDep communication panel within the deposition session for the entry in question. Once submitted, the revised model will be processed by wwPDB biocurators and a new version released. Versioning of PDB entries will be limited to changes in the coordinate files, with no changes permitted to the deposited experimental data. PDB versioning will be limited to one replacement per PDB entry per year, and three entries per Principal Investigator per year. For more, please visit the wwPDB news pages <https://www.wwpdb.org/news/news#5d3ef68aea7d0653b99c87fd>. -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Survey on EMBL-EBI's data resources (incl. PDBe, PDBe-KB, EMDB, EMPIAR, BioImage Archive)
Dear CCP4BB, The European Bioinformatics Institute (EMBL-EBI; https://www.ebi.ac.uk/) provides biological data resources to the worldwide scientific community. You are probably familiar with PDBe (https://pdbe.org/), EMDB (https://emdb-empiar.org/) and EMPIAR (https://empiar.org/) and possibly also with PDBe-KB (https://pdbe-kb.org/) and the recently launched BioImage Archive (https://www.ebi.ac.uk/bioimage-archive/). We strive to meet the data needs of biological researchers, understand how scientists use our data resources and improve the services we provide. Each year we invite the scientific community to complete a survey about their experiences using (or not using) EMBL-EBI's freely available data resources. We carefully analyze your responses and comments to understand how you use our data resources to prioritize our development and better serve the scientific community. We encourage you to fill out the survey even if you think you do not use our data resources: your responses are still of interest to us. It is important for us (the structural resources) to get a lot of responses from people with an interest in structural biology data (molecular, cellular, and beyond). The survey can be found here: https://www.surveymonkey.co.uk/r/2N99899 Please feel free to pass this email on to others who may have an interest in EMBL-EBI's data resources. Many thanks, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] REMINDER: Scientific Data Curator position (PDB and EMDB)
Dear CCP4BB, Just a gentle reminder of the scientific data curator position available at PDBe. The closing date for the post is Friday 5th July. For more information, please see: https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01403 Kind Regards, David Armstrong On 29/05/2019 08:20, John Berrisford wrote: Dear CCP4BB We are looking to recruit an expert structural biologist to join the PDBe curation team on the Wellcome Genome Campus near Cambridge. The work involves annotating preliminary PDB and EMDB submissions and extracting relevant biological information. The closing date for the post is 5th July 2019. For more information on the position, please visit: https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01435 Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 http://www.pdbe.org <http://www.pdbe.org/> http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] New PDBe-KB aggregated views of protein structure
*New PDBe-KB aggregated views of protein structure* We are delighted to announce the newprotein-centric aggregated views <https://www.ebi.ac.uk/pdbe/pdbe-kb/protein>, developed as part of our new collaborative resourceProtein Data Bank in Europe Knowledge Base (PDBe-KB) <https://www.ebi.ac.uk/pdbe/pdbe-kb/>. You can view the new pages at pdbe-kb.org/proteins <https://www.ebi.ac.uk/pdbe/pdbe-kb/proteins>. PDBe-KB is a community-driven resource managed by the PDBe team, collating functional annotations and predictions for structure data in the PDB archive, giving researchers a more comprehensive view of publicly available protein structure data. PDBe entry pages traditionally focus on single PDB entries, with limited information on entries that are related to the same macromolecule. The PDBe-KB team is proud to present a new type of entry page, that focuses on full length proteins instead of single PDB entries. Currently, you can use PDB or UniProt identifiers of proteins to display all the related PDB data, from the list of all the available PDB entries, to functional annotations of ligand binding sites, macromolecular interaction interfaces, and related publications. We would especially like to thank those members of CCP4bb that helped us in shaping the resource by providing feedback. We encourage you to continue to provide feedback <https://goo.gl/forms/55Xzc2BBT93uyp9g1> to ensure that we continue to develop this resource in a way that is most valuable for you all. If you would like more information about the new resource then please visit the PDBe-KB website <https://www.ebi.ac.uk/pdbe/pdbe-kb> or view our webinar <https://youtu.be/ZJksQS4vmuM>, which introduces you to our new pages. Many thanks, PDBe team -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge, CB10 1SD, UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Wednesday 3.30pm (UTC) - Webinar: PDBe-KB Aggregated views
On behalf of PDBe, I invite you to attend a webinar on the new PDBe Knowledge Base (PDBe-KB) resource. This webinar will introduce you to the new PDBe-KB Aggregated views: brand new pages presenting PDB data in a different context. For more information and to register for the webinar, please visit the following link: bit.ly/PDBe-KB-webinar Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Fwd: 2 EMDB Job Opportunities at EMBL-EBI
Please see the following job opportunities available with our colleagues at EMDB. Kind Regards, David Armstrong Forwarded Message Subject:2 EMDB Job Opportunities at EMBL-EBI Date: Tue, 22 Jan 2019 10:46:19 + From: Osman Salih To: 'David Armstrong' Hi Dave, Could you please circulate the following message to the CCP4 mailing list? Thanks and best wishes, Oz -- Dear CCP4, There are two fantastic opportunities to be part of the exciting EMDB Team at EMBL-EBI in Hinxton near Cambridge. EMBL-EBI is a world-leader in archiving and disseminating 3D biomacromolecular and cellular structure data and plays a key role in the dissemination of 3D electron microscopy (EM) data through the EMDB (emdb-empiar.org) and EMPIAR (empiar.org) public archives. Specifically, we are looking for: 1. A Scientific Programmer (https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01331) 2. A Data Scientist (https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01332) The closing dates for both positions are 6th February 2019. Good luck! EMDB EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD. UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] RNA pdb molecular weight
Dear Reza, The calculated molecular weight for each molecule in a PDB entry is given in the archive PDBx/mmCIF file. The weight in Daltons is given in the _entity.formula_weight category. Please see http://www.ebi.ac.uk/pdbe/entry-files/4tna.cif for an example file. Kind Regards, David On 16/11/18 16:19, Reza Khayat wrote: Hi, I’m not an RNA person. Can anyone suggest a method to calculate the mass of a RNA PDB? I’d like the protons to also be considered in the calculation. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
